自动化运行OrthoMCL

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git clone https://github.com/apetkau/orthomcl-pipeline.git

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cpanm BioPerl DBD::mysql DBI Parallel::ForkManager YAML::Tiny Set::Scalar Text::Table Exception::Class Test::Most Test::Warn Test::Exception Test::Deep Moose SVG Algorithm::Combinatorics

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$ perl scripts/orthomcl-pipeline-setup.pl
Checking for Software dependencies...
Checking for OthoMCL ... OK
Checking for formatdb ... OK
Checking for blastall ... OK
Checking for mcl ... OK
Wrote new configuration to orthomcl-pipeline/scripts/../etc/orthomcl-pipeline.conf
Wrote executable file to orthomcl-pipeline/scripts/../bin/orthomcl-pipeline
Please add directory orthomcl-pipeline/scripts/../bin to PATH

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$ mysql -u root -p 
Enter password: 
mysql> GRANT SELECT, INSERT, UPDATE, DELETE, CREATE, CREATE VIEW, INDEX, DROP on . to orthomcl;  #创建用户并授权 
mysql> set password for orthomcl@localhost = password('orthomcl');  #设置用户密码 
mysql> quit;

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$ perl scripts/orthomcl-setup-database.pl --user orthomcl --password orthomcl --host localhost --database orthomcl --outfile orthomcl.conf
Connecting to mysql and creating database **orthmcldb** on host orthodb with user orthomcl ...OK
database orthmcl created ...OK
Config file **orthomcl.conf** created.

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$ perl t/test_pipeline.pl -m orthomcl.conf -s fork -t /tmp
Test using scheduler fork

TESTING NON-COMPLIANT INPUT
TESTING FULL PIPELINE RUN 3
README:
Tests case of one gene (in 1.fasta and 2.fasta) not present in other files.
ok 1 - Expected matched returned groups file
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$ ./bin/orthomcl-pipeline
Error: no input-dir defined
Usage: orthomcl-pipeline -i [input dir] -o [output dir] -m [orthmcl config] [Options]
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